Contacts of the strand formed by residues 45 - 54 (chain I) in PDB entry 4EMG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with MSE 45 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14I VAL* 5.2 2.5 - - + -
22I VAL* 5.1 1.6 - - - -
24I VAL* 3.7 31.0 - - + -
36I LEU* 3.8 27.4 - - + -
38I ALA 3.2 6.1 - - - +
39I TYR* 3.9 8.3 - - + -
43I LEU* 3.5 8.5 + - + +
44I ASN* 1.3 81.0 - - - +
46I VAL* 1.3 61.5 + - - +
47I LEU* 4.2 10.3 - - + -
79I PHE* 3.4 5.2 - - - -
80I VAL* 2.7 51.1 + - + +
85I VAL* 3.3 34.1 - - + -
88I ILE* 3.8 27.1 - - + -
10J PRO* 4.5 2.9 - - - -
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Residues in contact with VAL 46 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36I LEU 3.9 0.2 - - - -
37I HIS* 2.9 32.6 + - + -
38I ALA* 3.0 21.1 + - + +
45I MSE 1.3 77.9 - - - +
47I LEU* 1.3 71.3 + - - +
77I MSE 3.9 29.6 - - + -
78I LEU 3.2 6.7 - - - +
79I PHE* 4.4 3.1 - - + -
9J GLU 5.1 0.7 - - - +
10J PRO* 3.5 32.5 - - + +
13J LEU* 3.8 26.7 - - + -
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Residues in contact with LEU 47 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I VAL* 4.1 11.0 - - + -
24I VAL* 4.2 12.3 - - + -
32I LEU* 3.9 39.9 - - + -
33I ASN 4.6 0.7 - - - -
34I GLY* 3.9 22.4 - - - +
35I ARG 3.4 0.9 - - - -
36I LEU* 4.0 27.1 - - + +
45I MSE 4.0 11.6 - - + -
46I VAL* 1.3 82.3 - - - +
48I GLY* 1.3 59.3 + - - +
50I ALA* 3.8 16.2 - - + +
77I MSE 3.5 2.3 - - - -
78I LEU* 2.7 45.6 + - + +
80I VAL* 4.2 6.1 - - + -
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Residues in contact with GLY 48 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I GLY* 3.5 1.0 - - - -
35I ARG* 2.8 35.1 + - - +
37I HIS* 3.6 26.7 + - - -
47I LEU* 1.3 71.4 - - - +
49I ASP* 1.3 74.9 + - - +
50I ALA 3.3 2.8 + - - -
76I GLU 3.4 7.4 - - - -
77I MSE 3.9 2.2 - - - -
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Residues in contact with ASP 49 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I ASN 4.0 4.3 - - - +
34I GLY* 4.0 2.8 - - - -
35I ARG* 5.6 4.9 - - + +
48I GLY* 1.3 74.3 - - - +
50I ALA* 1.3 61.1 + - - +
51I GLU* 4.0 0.5 + - - +
74I HIS* 3.4 26.5 + - - -
75I TYR 3.3 7.2 - - - -
76I GLU* 2.7 20.7 + - - +
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Residues in contact with ALA 50 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I LEU* 5.6 0.2 - - + -
33I ASN 3.0 12.8 - - - +
47I LEU* 3.8 31.6 - - + +
48I GLY 3.9 0.7 - - - -
49I ASP* 1.3 74.9 - - - +
51I GLU* 1.3 62.1 + - - +
74I HIS* 3.2 8.0 - - - -
75I TYR* 2.7 44.4 + - + +
78I LEU* 4.1 24.7 - - + -
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Residues in contact with GLU 51 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I LEU* 3.2 8.7 - - - +
33I ASN* 2.8 49.0 + - + +
49I ASP 4.0 0.6 + - - +
50I ALA* 1.3 75.3 - - - +
52I GLU* 1.3 63.3 + - - +
53I ILE* 3.7 22.7 - - + +
72I ARG* 2.7 39.3 + - + +
73I LYS 3.3 9.6 - - - +
74I HIS* 4.5 7.6 - - + +
75I TYR* 5.3 0.2 - - - -
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Residues in contact with GLU 52 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I ARG* 2.6 48.2 + - + -
31I GLU 3.4 4.0 - - - -
32I LEU* 3.7 16.8 - - + -
50I ALA 4.2 0.2 - - - -
51I GLU* 1.3 74.1 - - - +
53I ILE* 1.3 64.5 + - - +
54I VAL* 4.5 7.4 - - + -
71I ILE 3.8 0.9 - - - +
72I ARG* 3.3 6.8 - - - +
73I LYS* 2.8 42.7 + - + +
75I TYR* 2.7 40.7 + - + -
23J TYR* 4.7 2.6 + - - -
25J LYS* 5.2 0.5 - - - +
87J LEU* 3.9 12.2 - - - +
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Residues in contact with ILE 53 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I ASP 3.6 3.5 - - - +
31I GLU* 2.9 47.2 + - + +
33I ASN* 4.0 16.2 - - - +
51I GLU* 3.7 27.6 - - + +
52I GLU* 1.3 79.0 - - - +
54I VAL* 1.3 63.2 + - - +
55I THR* 3.8 22.1 + - + +
70I THR* 4.0 15.3 - - + +
71I ILE 3.8 2.5 - - - -
72I ARG* 3.4 35.4 - - + +
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Residues in contact with VAL 54 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29I ASP* 3.4 13.5 - - + +
30I ARG* 3.4 36.8 - - + +
52I GLU* 4.0 9.4 - - - +
53I ILE* 1.3 74.6 - - - +
55I THR* 1.3 69.6 + - - +
70I THR* 3.1 4.2 - - - -
71I ILE* 2.8 62.2 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il